February 20, 2013

AAPA 2013 abstracts

The program of the 2013 meeting of the American Association of Physical Anthropologists is now online (pdf). As always, there is plenty of interest here, so I'll just highlight a few titles that caught my eye; feel free to add more in the comments.

Haplogroup (hg) H dominates present-day Western European mitochondrial (mt) DNA variability (>40%), yet was less prevalent amongst early Neolithic farmers (~19%) and virtually absent in Mesolithic hunter-gatherers. To investigate this haplogroup’s significance in the maternal population history of Europeans we employed novel techniques such as DNA immortalization and hybridization-enrichment to sequence 39 hg H mt genomes from ancient human remains across a transect through time in Neolithic Central Europe.
The results of our population genetic analyses reveal that the current patterns of diversity and distribution of hg H were largely established during the Mid-Neolithic, but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers, which expanded out of Iberia in the Late Neolithic (~2800 BC). Using a strict diachronic approach allowed us to reconcile ‘real-time’ genetic data from the most common European mtDNA hg with cultural changes that took place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. This revealed the Late Neolithic (2800-2200 BC) as a dynamic period that profoundly shaped the genetic landscape of modern-day Europeans.
Furthermore, linking ancient hg H genome sequences to specific points in time by using radiocarbon dates as tip calibrations allowed us to reconstruct a precise lineage history of hg H and to calculate a mutation rate 45% higher than traditional estimates based on the human/chimp split.

Preliminary research on hereditary features of Yinxu Population.

... The 37 individuals sampled in this study have been discovered in middle to small size burials, and therefore constitute a representative sample to study Yinxu commoners’ society. Mitochondrial DNA analysis showed that the Yinxu population included the haplogroups D, G, A, C, Z, M10, M*, B, F and N9a. According to the analysis of molecular variance, the distribution frequency and the rare published data, the Yinxu population shows a closest genetic affinity with the populations of Dadianzi and Zhukaigou early Bronze Age sites (Inner Mongolia), but a more distant relation to the historical period populations. The Yinxu population is also very similar to the modern northern Han Chinese. ...

Investigating lactase persistence in a Medieval German cemetery: A step towards understanding the rise of the European lactase persistence polymorphism (-3910C/T).

Previous ancient DNA-based studies on the Neolithic found that the incidence of LP falls below detection levels in most regions. Our research shows that between the Neolithic and Medieval periods, the frequency of LP rose from near 0% to over 50%. Also, given that the frequency of LP genotypes in modern-day Germany is estimated at 78.5%, our results indicate that rather than being stable by the Medieval period, the lactase persistent genotype has continued to increase in frequency over the last 1000 years. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistent trait and its global cultural implications.

New Neanderthal remains from Kalamakia cave, Mani peninsula, Southern Greece.Peeling back the layers: additional evidence for the date of the Petralona skull (Homo heidelbergensis), Greece.

,.. We conclude that there is no white sinter deposited directly on the skull and therefore the initial date of the skull given by Henning et al. and Grun’s revised date of ca. 200 ka are correct.

Analysis of archaic introgression in Ötzi the Tyrolean Iceman, a 5300 year-old prehistoric modern human.

... We carried out a series of comparisons to address these questions. By examining the Neandertal similarity of individuals from the 1000 Genomes Project, we have substantially expanded the sample of Neandertal-human comparisons. We also examined the genome of the Tyrolean Iceman, a European from approximately 5300 years ago. This is the first comparison of Neandertal genomes to the genome of a prehistoric modern human individual.

A quantitative approach for late Pleistocene hominin brain size.

... The results of our study show that Neanderthals have smaller brains than the Pleistocene AMH despite the fact that the latter are smaller in body mass. However, the Holocene AMH (7 populations) have smaller brain sizes than those of Neanderthals. ...

Re-evaluating the functional and adaptive significance of Neandertal nasofacial anatomy.

... Among Middle and Late Pleistocene Homo, there is evidence that nasal morphology varies with climate, albeit within an archaic architectural nasofacial framework. Neandertal internal nasal dimensions are greater in both height and length than archaic humans from sub-Saharan Africa. Furthermore, while other aspects of the nose are relatively broad, superior internal breadth dimensions in Neandertals are narrowed relative to sub-Saharan archaics. These differences parallel those seen in modern humans, indicating that Neandertals had an increased capacity for nasal heat and moisture exchange over their African counterparts and thus exhibit clear evidence for cold-climate adaptation.

12 comments:

Do you take requests? Could you remember to comment on the following study when it comes out? It looks like they tested a lot of samples, 400 mtdna and 250 y-dna, and most significantly, the abstract implies they used lots of recently found y-SNPs for determining the haplogroups.

"...the Yinxu population shows a closest genetic affinity with the populations of Dadianzi and Zhukaigou early Bronze Age sites (Inner Mongolia), but a more distant relation to the historical period populations."

Interesting result and seems to reinforce something already known, that in the second millennium BCE the cultures represented at Dadianzi and Zhukaigou were either in contact with the Shang or were otherwise closely related to the Shang. Zhukaigu was apparently influenced by the Qijia culture, the most likely vector for the introduction of bronze technology into the Chinese heartland.

In addition to possessing relatively advanced metallurgy, the Qijia bred horses and practiced oracle divination, all cultural traits that were highly developed in the Shang.

Concerning the abstract discussing mtDNA H: Population replacements are one side of the coin, but surely a parsimonious explanation for the rise of R1b and mtDNA H in Europe since the Mesolithic is the advantages these confer respectively in disease protection and sperm function. For instance R1b is likely under strong selective pressure for the protection it provides against coronary disease:

And mtDNA H is likely under strong selection for the protection it confers in men that have this haplogroup against low sperm motility:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1287528/

Quite simply these are advantageous alleles that may still be undergoing positive selection, rather like lactase persistence, which has been increasing in frequency even since the middle ages. It's easy to imagine how R1b would be swept to near-fixation in any farming population that consumed a lot of saturated fats and carbohydrates, at least as long as the old guys in the corners of their huts who *haven't* had heart attacks by age 50 are still of some use. Especially if their healthy mtDNA H sperm was still making some babies in their densely populated farming villages.

Your analysis doesn't fit the data. Europe has current haplogroup distributions by the end of the Copper Age, more or less and then is stable. The initial Neolithic has been shown in several ancient DNA studies to be abrupt. There is good archaeological and physical anthropology evidence for an abrupt change in the Copper Age. But, sperm motility and middle age heart health improvements, even if they are present, don't have that profile, those are fitness enhancements that would provide small percentage fitness enhancements over many generations not abrupt fitness enhancements followed by statsis (besides which mtDNA may have an impact on metabolism but probably not immune function). You do see that kind of continuous fitness enhancement right into the last thousand years for lactose persistence, you don't see that for NRY-DNA and mtDNA haplogroups.

The evidence is a much better fit to Y-DNA R1b and mtDNA H expanding as a package on the strength of Belll Beaker (including successor cultures in continuity with it) having technological, cultural and political organization advantages than it is for them expanding in frequency mostly as a result of intrinsic fitness enhancement value.

"These differences [Neandertal internal nasal dimensions are greater in both height and length than archaic humans from sub-Saharan Africa] parallel those seen in modern humans, indicating that Neandertals had an increased capacity for nasal heat and moisture exchange over their African counterparts and thus exhibit clear evidence for cold-climate adaptation".

Are 'these differences' a result of introgression from Neanderthals or the result of subsequent evolution in Europe? It would be very interesting to know the gene(s) involved, and their ancestry.

I think you missed half of my meaning. To repeat: "Population replacements are one side of the coin..."; this comment implies roughly equal weighting for two concepts. I do not deny the simple appeal of linking R1b to Bell Beaker based on the currently available evidence. Bell Beaker was clearly a dispersive phenomenon, and there are any number of isotopic studies we could reference that would support people migrating during these and earlier time periods, for example:http://www.pasthorizonspr.com/index.php/archives/02/2013/confirmation-that-near-east-farmers-bring-agriculture-to-europe

However, you are subordinating the importance of biologically adaptive fitness operating under the influence of a radical change in lifestyle and environment (i.e. as brought on by a transition to farming, a major "adaptive stress"), to the cultural advantage provided by early metallurgy and the adjusted social structure that was built along with it. The decline in individual fitness of early Neolithic individuals relative to their Mesolithic predecessors is archaeologically obvious even at the skeletal level, therefore it’s evident these people were under strong selective pressure.

To discuss the change in haplogroup frequencies over time: Under an adaptive stress scenario the period of most rapid change in allele frequencies would be during the initial onset of the stressor, when the least advantageous genes are rapidly replaced. This is the common scenario during an epidemic, classic survival of the newly fittest. In the currently discussed case I can envision any mixed haplogroup society that adopted farming and its attendant biological stressors would strongly select for advantageous alleles during the early adaptive period. After the initial Neolithic rollover you’re left with a set of “nearly equally good” genes by the Bronze Age that can then compete with each other over time both biologically and through culture. This of course is against the backdrop of migrating, mutually competing groups you and the majority of commentators focus on.

I would further argue against your position that minor fitness advantages, like cardiovascular health and sperm function would not be strongly selected for over time. This is admittedly challenging to quantify, however it makes sense given real-life parallels.

In short, the biological fitness of various mtDNA and Y groups should definitely be considered. Agricultural diseases both parasitic and intrinsic are still affecting us today. This would certainly have been the case in the past, and adding the element of biological fitness would reduce the R1b cultural supermen / mtDNA H superwomen, “everyone was genocidal and bred like a Pharaoh” thrust of the neutral biologically adaptive camp.

Are there studies investigating the effect of the antibodies present in milk on the immune system and immunization?

With all the pandemics ravaging through Europe, I could see a potentially significant benefit, there.

As to the genetic impact of Bell Beakers, let's not forget that they were only present in parts of Europe, and in central Europe, even where they were, their settlement density was very low (~10% - 20% of that of regular agriculturalists).

Autoimmune diseases in general are more common in women than in men. An example of this would be Multiple sclerosis which is more common among women further away from the equator. Kind of makes me wonder if European Mesolithic Hunter-Gatherers were also in possession of these unfavorable mutations or if the tendency to MS is the lack of appropriate adaption over time from people coming "recently" from southerly regions.

"The decline in individual fitness of early Neolithic individuals relative to their Mesolithic predecessors is archaeologically obvious even at the skeletal level, therefore it’s evident these people were under strong selective pressure."

Doesn't that show the opposite? If the neolithics were a lot less fit than the mesolithics doesn't that imply it had become easier to survive so even if you had a few physical flaws you could still get by while the H-Gs had to be more flawless to survive?

There is a clear correlation of MS with lack of vitamin D. So, yes, southerners with dark skin would tend to suffer from it in the north/ foggy NW, unless they had a diet high in fish/ sea mammals or drank a lot of milk.

However, MS is not sufficiently prevalent to cause selective pressure - it's more of a "diagnostically valuable" side-effect.

Maybe I am wrong, but I think female selection in context with nutriment is just a byproduct of specialized societies. In traditional societies there is a lot of internal pressure and competition among females themselves/offspring, so the acceptance of a female coming from outside of their cultural realm would be low among the females already well established in a specialized society, like in a dairy producing society. So it is likely that the outsider and her offspring would have less had access to food. Would kind of explain why MS with its genetic inherited component is more common in "white" women, because this group of women would be the descendents of a well established and specialized group of females.

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